1. Sent to the war department and given a capture number
stenciled somewhere on the flag. These were returned to the states of origin or the MOC the most part in 1905.

2. Given as gifts by Stanton, or borrowed from the war department and never returned. No one knows their fate, but most probably in private collections.

3. Captured and kept as war souveniers by various individual soldiers. Many of these flags were later donated to the state governments, usually be descendents of those who captured the flag. These flags are the lawful propeerty of the individual states and can be found in their military museums or archives. This is the source of the IL Confederate flag collection.

4. Remain in private hands. These come up for auction from time to time and sell in the tens to hundreds of thousands of dollars, depending on the flag. A couple of years ago, Gen. Stuarts HQ flag sold for a kings ransom IIRC

5. In the collection of the Chicago Historical Society. They are very closed mouthed about their collection, rarely display any of them and generally provide little or no information about their collection. It is believed to exceed a hundred flags. It is known for example, that they hold the flag of the 8th Texas, Terry's Texas Rangers.

In addition many uncaptured flags were secreted away rather than be surrendered. No one knows the ultimate fate of these.